Extremophiles最新文献_第2页

Variations on a theme: non-canonical DUF3494 ice-binding proteins. 一个主题的变体：非规范DUF3494冰结合蛋白。

IF 2.6 3区生物学

Extremophiles Pub Date : 2024-12-13 DOI: 10.1007/s00792-024-01374-y

James A Raymond

{"title":"Variations on a theme: non-canonical DUF3494 ice-binding proteins.","authors":"James A Raymond","doi":"10.1007/s00792-024-01374-y","DOIUrl":"10.1007/s00792-024-01374-y","url":null,"abstract":"Among the many ice-binding proteins (IBPs) found in microorganisms (bacteria, archaea, fungi and algae), the canonical DUF3494 beta-barrel type is the most common. Until now, little variation has been found in this structure: an initial coil leads into an alpha helix that directs the following coils into a reverse stack, with the final coil ending up next to the initial coil. Here, I show that there exist many bacterial proteins whose AlphaFold-predicted structures deviate from the DUF3494 structure so that they are not recognized as belonging to an existing DUF or Pfam family. In these non-canonical DUF3494 (ncDUF3494) proteins, the number of coils in the alpha helix is highly variable, often being as high as 14. The putative ice-binding sides of each of 13 proteins modeled have a well-aligned row of hydrophilic residues, with spacings that are close to the repeat distance on the ice a-axis. A recombinant protein made for one of the proteins showed that it had ice-binding activity, even in the µg/ml range. The ncDUF3494 proteins appear to be found only in bacteria, the great majority of which live in icy habitats. C-terminal PEP-Cterm motifs, which are rare in DUF3494s, are present in most of the ncDUF3494s, possibly indicating a secretory function. The relatively narrow distribution of ncDUF3494 proteins suggests that they are a later development in DUF3494 evolution.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"29 1","pages":"8"},"PeriodicalIF":2.6,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11645318/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142817296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterization of a family IV esterase from extremely halophilic archaeon Haloarcula japonica. 极嗜盐古菌日本盐环菌IV家族酯酶的鉴定。

IF 2.6 3区生物学

Extremophiles Pub Date : 2024-12-03 DOI: 10.1007/s00792-024-01370-2

Hiromichi Kato, Shota Ambai, Fumiya Ikeda, Koji Abe, Satoshi Nakamura, Rie Yatsunami

引用次数: 0

Biological treatment of methyl orange dye and textile wastewater using halo-alkaliphilic bacteria under highly alkaline conditions. 在高碱性条件下利用卤代嗜碱性细菌对甲基橙染料和纺织废水进行生物处理。

IF 2.6 3区生物学

Extremophiles Pub Date : 2024-11-27 DOI: 10.1007/s00792-024-01369-9

Gunisha Wadhawan, Anshu Gupta

{"title":"Biological treatment of methyl orange dye and textile wastewater using halo-alkaliphilic bacteria under highly alkaline conditions.","authors":"Gunisha Wadhawan, Anshu Gupta","doi":"10.1007/s00792-024-01369-9","DOIUrl":"https://doi.org/10.1007/s00792-024-01369-9","url":null,"abstract":"As the textile wastewater is highly saline and has high pH it is important to employ extremophilic microbes to survive in harsh conditions and provide effective bioremediation of textile dyes. This study aims to find a sustainable solution for dye removal by investigating the potential of an indigenously isolated bacterium, Nesterenkonia lacusekhoensis EMLA3 (halo-alkaliphilic) for treatment of an azo dye, methyl orange (MO) and textile effluent. MO dye decolorization studies were conducted using mineral salt media (MSM) by varying incubation time (0-120 h), initial dye concentration (50-350 mg/L), pH (7.0-12.0), inoculum dose (3-10%), agitation (stationary, 100 rpm and 200 rpm), and temperature (20-55 °C). Dye removal by the bacterium for 50 mg/L of dye was > 97.0% within 72 h of incubation at pH 11.0 in stationary condition. Bacterium had excellent reusability i.e. > 97% dye removal for up to 5 cycles. Moreover, bacterium has the potential for co-removal of chromium (VI) (3.5-28 mg/L), and also almost complete dye removal in presence of high amount of NaCl. Liquid chromatography-mass spectrometry showed degradation as the mechanism of dye removal. Application of the bacterium to MO dye spiked real textile wastewater showed excellent dye removal. Phyto-toxicity assessment conducted on Vigna radiata and Triticum aestivum seeds, showed 100% germination of biotreated textile wastewater indicating its reuse potential.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"29 1","pages":"6"},"PeriodicalIF":2.6,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142727124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Lawrence I. (Larry) Hochstein a researcher dedicated to halophilic microorganisms of all types and environments. Lawrence I. (Larry) Hochstein 致力于研究各种类型和环境中的嗜卤微生物。

IF 2.6 3区生物学

Extremophiles Pub Date : 2024-11-26 DOI: 10.1007/s00792-024-01364-0

Russell H Vreeland, Aharon Oren, Antonio Ventosa

引用次数: 0

Characterization of prokaryotic communities from Italian super-heated fumaroles. 意大利超高温火成岩原核生物群落的特征。

IF 2.6 3区生物学

Extremophiles Pub Date : 2024-11-23 DOI: 10.1007/s00792-024-01371-1

Alessia Rossi, Irene Barbagli, Claudia Vannini

{"title":"Characterization of prokaryotic communities from Italian super-heated fumaroles.","authors":"Alessia Rossi, Irene Barbagli, Claudia Vannini","doi":"10.1007/s00792-024-01371-1","DOIUrl":"https://doi.org/10.1007/s00792-024-01371-1","url":null,"abstract":"Among extremophiles, thermophile microorganisms from geothermal sites have been widely studied. Nevertheless, our knowledge is still relatively poor on microbial communities colonizing fumaroles, which are super-ephemeral habitats, characterized by an only intermittent presence of water. Here we characterized by metabarcoding both bacterial and archaeal communities from hot spring waters and biofilms, together with dry and wet fumaroles, of a geothermal basin in central Italy. Taxa composition of the analyzed samples mirrored that of previous studies, with Thermoproteota dominating among Archaea, while high percentages of thermophiles and spore-forming organisms were retrieved for Bacteria. Cyanobacteriota were the dominant group in biofilms. Community structure was different in the two domains, with highly selected communities of Archaea, less diversified than bacterial ones. Linear regression analyses highlighted significant correlations between diversity and environmental parameters in dry, but not in wet fumaroles. Although ASV numbers displayed different trends for the two different prokaryotic domains (positive correlation with pH for Bacteria, negative correlation for both pH and T for Archaea), such results indicate that even an extremely ephemeral presence of water can influence the importance of temperature and pH as drivers for microbial community structure.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"29 1","pages":"4"},"PeriodicalIF":2.6,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Increase of ATP synthesis and amino acids absorption contributes to cold adaptation in Antarctic bacterium Poseidonibacter antarcticus SM1702^T. 增加 ATP 合成和氨基酸吸收有助于南极波塞冬杆菌 SM1702T 对寒冷的适应。

IF 2.6 3区生物学

Extremophiles Pub Date : 2024-11-22 DOI: 10.1007/s00792-024-01372-0

Wen-Yue Xu, Sha-Sha Liu, Xiao-Han Guo, Peng Wang, Chun-Yang Li, Li Liao, Qi-Long Qin

{"title":"Increase of ATP synthesis and amino acids absorption contributes to cold adaptation in Antarctic bacterium Poseidonibacter antarcticus SM1702T.","authors":"Wen-Yue Xu, Sha-Sha Liu, Xiao-Han Guo, Peng Wang, Chun-Yang Li, Li Liao, Qi-Long Qin","doi":"10.1007/s00792-024-01372-0","DOIUrl":"10.1007/s00792-024-01372-0","url":null,"abstract":"Numerous psychrophiles inhabit the cold environments that are prevalent across the global biosphere. The adaptation of psychrophiles to cold conditions has been widely studied in strains from the archaeal phylum Euryarchaeota and the bacterial class Gamma-proteobacteria. However, given the vast diversity of microorganisms in cold environments, many microbial lineages with potentially unique cold-adaptation strategies remain largely unexplored. This study investigates the cold responses of the Antarctic strain Poseidonibacter antarcticus SM1702T, a cold-adapted bacterium belonging to the class Epsilon-proteobacteria within the phylum Campylobacterota. Proteomic analysis revealed that this strain responds to low temperatures by overexpressing proteins involved in energy production and amino acid transport. Experimental results confirmed that intracellular ATP concentrations increased at low temperatures compared to higher temperatures. Low temperatures significantly reduced the strain's amino acid absorption rates, a condition that was mitigated by increased expression of membrane transporters. We propose that the impairment of membrane protein function due to low temperatures is the primary factor affecting cell growth. As a result, the strain enhances ATP synthesis and upregulates membrane transporter expression to counteract cold stress. These findings contribute to a deeper understanding of cold adaptation strategies in psychrophiles.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"29 1","pages":"3"},"PeriodicalIF":2.6,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142686633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microbial and mineralogical characterization of the alkaline Chae Son hot spring, Northern Thailand. 泰国北部碱性 Chae Son 温泉的微生物和矿物特征。

IF 2.6 3区生物学

Extremophiles Pub Date : 2024-11-21 DOI: 10.1007/s00792-024-01373-z

C Sriaporn, S Komonjinda, N Klayposri, K Phinyo, J Pekkoh, S Awiphan, T Chanprom

{"title":"Microbial and mineralogical characterization of the alkaline Chae Son hot spring, Northern Thailand.","authors":"C Sriaporn, S Komonjinda, N Klayposri, K Phinyo, J Pekkoh, S Awiphan, T Chanprom","doi":"10.1007/s00792-024-01373-z","DOIUrl":"https://doi.org/10.1007/s00792-024-01373-z","url":null,"abstract":"Early characterizations by morphological identification through light microscopy only revealed the presence of a few microbial lineages and the majority of microbial community at the Chae Son hot spring remains uncharacterized. Therefore, this study aims to examine thermophilic microbial communities at the Chae Son hot spring using next-generation sequencing, including investigating hot spring mineralogy. Results suggest that the Chae Son hot spring (49-75 °C, pH = 6.5-7.0) precipitates digitate structures which comprise mainly silica, and that microbial permineralization is primarily through silicification. Alternating layers of mineralized microbial biofilms and silica were observed in digitate sinter cross-sections, contributing to the build-up of microstromatolites. Molecular results revealed that phylogenetically distinct members of photoautotrophic taxa, Chloroflexota and Cyanobacteriota, dominated spring microbial communities (63.19% relative abundance). Potential primary production processes were mainly through photoautotrophy, with minor lithoautotrophic activities (e.g., sulfur cycling and nitrogen cycling). Moreover, overall microbial community and Cyanobacteriota population alpha diversities significantly decreased with increased temperatures. However, no significant correlation was identified between Chloroflexota population diversity and temperatures. This study provides an update on the microbial community using a high-throughput next-generation sequencing technology, including the mineralogy of the Chae Son hot spring, Northern Thailand.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"29 1","pages":"2"},"PeriodicalIF":2.6,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Insights into the role of cyclopropane fatty acid synthase (CfaS) from extreme acidophile in bacterial defense against environmental acid stress. 洞察极端嗜酸菌环丙烷脂肪酸合成酶（CfaS）在细菌防御环境酸胁迫中的作用。

IF 2.6 3区生物学

Extremophiles Pub Date : 2024-11-16 DOI: 10.1007/s00792-024-01368-w

Wenbo Hu, Xingyu Huo, Tengfei Ma, Zhigang Li, Tianyou Yang, Hailin Yang, Shoushuai Feng

{"title":"Insights into the role of cyclopropane fatty acid synthase (CfaS) from extreme acidophile in bacterial defense against environmental acid stress.","authors":"Wenbo Hu, Xingyu Huo, Tengfei Ma, Zhigang Li, Tianyou Yang, Hailin Yang, Shoushuai Feng","doi":"10.1007/s00792-024-01368-w","DOIUrl":"https://doi.org/10.1007/s00792-024-01368-w","url":null,"abstract":"The cell membrane remodeling mediated by cyclopropane fatty acid synthase (CfaS) plays a crucial role in microbial physiological processes resisting various environmental stressors, including acid. Herein, we found a relatively high proportion (24.8%-28.3%) of cyclopropane fatty acid (CFA) Cy-19:0 in the cell membrane of a newly isolated extreme acidophile, Acidithiobacillus caldus CCTCC AB 2019256, under extreme acid stress. Overexpression of the CfaS encoding gene cfaS2 in Escherichia coli conferred enhanced acid resistance. GC-MS analysis revealed a 3.52-fold increase in the relative proportion of Cy-19:0 in the cell membrane of the overexpression strain compared to the control. Correspondingly, membrane fluidity, permeability and cell surface hydrophobicity were reduced to varying degrees. Additionally, HPLC analysis indicated that the overexpression strain had 1.54-, 1.42-, 1.85-, 1.20- and 1.05-fold higher levels of intracellular glutamic acid, arginine, aspartic acid, methionine and alanine, respectively, compared to the control. Overall, our findings shed light on the role of CfaS derived from extreme acidophile in bacterial defense against environmental acid stress, potentially facilitating its application in the design and development of industrial microbial chassis cells for organic acid production.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"29 1","pages":"1"},"PeriodicalIF":2.6,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome-based classification of Halobellus rubicundus sp. nov., a novel extremely halophilic archaeon isolated from a Korean solar saltern. 基于基因组的 Halobellus rubicundus sp.

IF 2.6 3区生物学

Extremophiles Pub Date : 2024-11-06 DOI: 10.1007/s00792-024-01367-x

Chi Young Hwang, Eui-Sang Cho, In-Tae Cha, Ki-Eun Lee, Eun-Young Lee, Myung-Ji Seo

{"title":"Genome-based classification of Halobellus rubicundus sp. nov., a novel extremely halophilic archaeon isolated from a Korean solar saltern.","authors":"Chi Young Hwang, Eui-Sang Cho, In-Tae Cha, Ki-Eun Lee, Eun-Young Lee, Myung-Ji Seo","doi":"10.1007/s00792-024-01367-x","DOIUrl":"10.1007/s00792-024-01367-x","url":null,"abstract":"A novel extremely halophilic archaeon designated, MBLA0158T, was isolated from a solar saltern in Sorae, Republic of Korea. The colonies are red-pigmented, Gram-stain-negative, pleomorphic, non-motile, and lysed in distilled water. The strain grows at 25-45 °C (optimum, 37 °C), in 15-30% (w/v) NaCl (optimum, 20%) and 0.1-1.0 M Mg2+ (optimum, 0.2-0.3 M) at pH 6.0-10.0 (optimum, 7.0-8.0). Comparative analysis based on the 16S rRNA gene sequence revealed that this strain is most closely related to the Halobellus inordinatus YC20T with a sequence identity of 96.0%. Strain MBLA0158T contained phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester as major polar lipids. The genome size is 3.29 Mb and the DNA G + C content is 66.9 mol%. Phylogenomic analysis confirmed that strain MBLA0158T is distinct from previously reported type strains of the genus Halobellus. Pan-genome analysis showed that strain MBLA0158T contains 419 genes that are not present in other type strains of the genus Halobellus. Based on overall analyses, strain MBLA0158T is considered to represent a new species of the genus Halobellus, for which the name Halobellus rubicundus sp. nov. is proposed. The type strain is MBLA0158T (= KCTC 4318T = JCM 36642T).","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"28 3","pages":"49"},"PeriodicalIF":2.6,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142589886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica. 古细菌的糖醇降解：Haloarcula hispanica 对甘露醇和山梨醇的吸收和降解。

IF 4.6 3区生物学

Extremophiles Pub Date : 2024-10-28 DOI: 10.1007/s00792-024-01365-z

Marius Ortjohann, Peter Schönheit

{"title":"Sugar alcohol degradation in Archaea: uptake and degradation of mannitol and sorbitol in Haloarcula hispanica.","authors":"Marius Ortjohann, Peter Schönheit","doi":"10.1007/s00792-024-01365-z","DOIUrl":"10.1007/s00792-024-01365-z","url":null,"abstract":"The halophilic archaeon Haloarcula hispanica utilizes the sugar alcohols mannitol and sorbitol as carbon and energy sources. Genes, enzymes, and transcriptional regulators involved in uptake and degradation of these sugar alcohols were identified by growth experiments with deletion mutants and enzyme characterization. It is shown that both mannitol and sorbitol are taken up via a single ABC transporter of the CUT1 transporter family. Then, mannitol and sorbitol are oxidized to fructose by two distinct dehydrogenases. Fructose is further phosphorylated to fructose-1-phosphate by a haloarchaeal ketohexokinase, providing the first evidence for a physiological function of ketohexokinase in prokaryotes. Finally, fructose-1-phosphate is phosphorylated via fructose-1-phosphate kinase to fructose-1,6-bisphosphate, which is cleaved to triosephosphates by a Class I fructose-1,6-bisphosphate aldolase. Two distinct transcriptional regulators, acting as activators, have been identified: an IclR-like regulator involved in activating genes for sugar alcohol uptake and oxidation to fructose, and a GfcR-like regulator that likely activates genes involved in the degradation of fructose to pyruvate. This is the first comprehensive analysis of a sugar alcohol degradation pathway in Archaea.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"28 3","pages":"48"},"PeriodicalIF":4.6,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11519228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142521505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0